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Author: ApressGryffinWinkler

week_1/chapter_21/makeProjectFS

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+#!/bin/bash
+
+# given a project name as argument
+# to this executable script,
+# bash instructs machine to make
+# a project filesystem for the project
+# in the project directory in one's
+# home directory.
+# if the project directory doesn't exist,
+# the machine will create it.
+
+# initialization
+PROJPATH=$HOME/project
+PROJ=$1
+
+mkdir -p "$PROJPATH"/"$PROJ"/data/raw     
+mkdir -p "$PROJPATH"/"$PROJ"/data/processed     
+
+
+mkdir -p "$PROJPATH"/"$PROJ"/figure/exploratory
+mkdir -p "$PROJPATH"/"$PROJ"/figure/final
+
+
+mkdir -p "$PROJPATH"/"$PROJ"/script/raw
+mkdir -p "$PROJPATH"/"$PROJ"/script/final
+
+
+mkdir -p "$PROJPATH"/"$PROJ"/text/readme
+mkdir -p "$PROJPATH"/"$PROJ"/text/text_of_analysis

week_1/chapter_23/getTop10IPHits

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+#!/bin/bash
+
+# initialization
+WEBLOG=$1
+
+# given a path to a web log, returns the top 10 ip browsers
+# with the most hits within the time span covered by the web log,
+# as well as the hit count for each.
+gawk '{print $1}' "$WEBLOG"|# print out only column 1 of each record in weblog
+sort |# make identical ip addrs contiguous in output
+uniq -c |# for each group of contiguous ip addrs, print single instance plus count
+sort -n |# numerically sort, by default in ascending order
+tail

week_11_1/bash_interactive_script.sh

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+#!/bin/bash
+
+# an infinite loop. in this example, only the user's input of an empty string
+# --- essentially, hitting RETURN instead of entering a project name when
+# prompted --- will cause the program counter to leave the while loop.
+
+while true; do # two statements on the same line are separated by a semicolon
+               # here, "do" marks the start of the while loop's block of code,
+               # while "done" below marks the end of it.
+
+    # at the top of the loop, we prompt the user for input from the command line
+    # and assign the input string to the variable PROJ
+    # -p means "prompt"
+    # "read without -r will mangle backslashes." ---shellcheck
+    read -pr "please give a project name: " PROJ
+    
+    # next, we test whether the user's input satisfies the condition
+    # to drop out of the infinite loop ---
+    # in other words, has the user hit ENTER or RETURN,
+    # (which generates the empty string),
+    # instead of entering a project name?
+    if [[ "$PROJ" == "" ]]
+    then
+        break # if the value of PROJ is the empty string, break out of while loop
+    fi
+    
+    # otherwise, the user has entered a project name.
+    # here, we tell the bash interpreter to make a directory
+    # in the working directory with the project name as its name
+    mkdir "$PROJ"
+
+done # end of while loop
+
+echo "and now we're out of the loop!"

week_11_1/bash_soln_find_all_words_you_can_make_with_calculator.sh

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+#!/bin/bash
+
+DICT=/usr/share/dict/american-english
+
+# extended grep, case-insensitive matches
+grep -Ei "^[BEHILOS]*$" $DICT

week_11_1/bash_soln_transform_fasta_records_into_1_record_per_row.sh

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+# lines 4-7 to "linearize the sequences"
+# from https://www.biostars.org/p/17680/ by Frédéric Mahé
+# Creative Commons License
+zcat All-Unigene.fa.zip |# read fasta recordset in zipped file into memory
+sed -E -e 's/(^>.*$)/#\1#/' |# use egrep; enclose 1st line in each record with hash marks
+tr -d "\n" |# delete newline characters
+tr "#" "\n" |# replace hash symbols with newline characters
+sed -e '/^$/d' |# delete empty lines
+tr -d "\n" |# delete newline characters --- fasta record separator (>) is in place
+tr '>' "\n" |# replace > with newline characters
+sed -e 's/%/% /' |# insert a space after the percent sign. space is field separator.
+tr -s ' ' |# replace each sequence of a repeated character with a single occurrence.
+sed -e '/^$/d' # delete empty lines
+

week_11_1/get_web_client_hits

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+#!/bin/bash
+
+http=$1
+
+wget -O - $http | cat | gawk '{print $1}'| sort | uniq -c | sort -n | tail -1

week_11_1/makeProjFS

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+#!/bin/bash
+
+PROJPATH=$HOME/project
+PROJ=$1
+
+mkdir -p "$PROJPATH"/"$PROJ"/data/raw
+mkdir -p "$PROJPATH"/"$PROJ"/data/processed
+
+mkdir -p "$PROJPATH"/"$PROJ"/figure/exploratory
+mkdir -p "$PROJPATH"/"$PROJ"/figure/final
+
+mkdir -p "$PROJPATH"/"$PROJ"/script/raw
+mkdir -p "$PROJPATH"/"$PROJ"/script/final
+
+mkdir -p "$PROJPATH"/"$PROJ"/text/readme
+mkdir -p "$PROJPATH"/"$PROJ"/text/text_of_analysis

week_11_1/say_hello_world

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+#!/bin/bash
+
+echo "hello, world!"

week_11_1/spellchecker

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+#!/bin/bash
+
+# initialization
+DICT=/usr/share/dict/american-english
+MYDICT=~/my_dict
+
+# to do: create my_dict is it doesn't exist
+
+tr -d '[:punct:]' | # delete punctuation
+tr -s ' ' '\n' | # replacing spaces with newline characters 
+sort | # alphabetically sort the words in the input string
+uniq| # remove multiple instances of the same word
+egrep -xvf $DICT | # compare entire lines, return complement, run against dictionary file
+tr '[:upper:]' '[:lower:]' | # replace all uppercase letters with lowercase equiv. 
+egrep -xvf $DICT | # remove common words that are uppercased in input string 
+egrep -xvf $MYDICT # remove entries in our personal dictionary file

week_11_3/dec_frac2bin_frac.py

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+''' chapter 42, Algorithm: Converting Positive Decimal Fractions Into Binary Fractions
+'''
+
+def dec_frac2bin_frac(dec_frac: float, num_bin_digits: int = 10) -> str:
+    ''' Given a positive fractional float as input,
+        returns its base-2 equivalent as a string.
+        A second argument is the number of digits
+        in the binary fraction. The default is 10
+        digits.
+        --------
+        examples
+        --------
+        >>>dec_frac2bin_frac(.75)
+        '0.1100000000'
+        >>>dec_frac2bin_frac(.1, 20)
+        '0.00011001100110011001'
+    '''
+    # garbage filters
+    assert isinstance(dec_frac, float), \
+        "dec_frac must be a positive fraction."
+    # if dec_frac is a positive fraction,
+    # the subtraction below yields zero.
+    # we assert dec_frac must be a positive fraction
+    # so we coerce that zero to a bool (False),
+    # and negate it to True.
+    # Other differences evaluate as False.
+    assert not dec_frac - (dec_frac % 1), \
+        "dec_frac must be a positive fraction."
+
+    # implementation of algorithm
+    # initialization
+    running_sum, bin_frac = 0, '0.'
+
+    # iterate through the positions of
+    # the binary fraction. for each position,
+    # calculate its base-10 value, then test
+    # whether or not it contributes to the value
+    # of the decimal fraction.
+    for position in range(1, num_bin_digits+1):
+        pos_value = 2**-(position)
+        if (running_sum + pos_value) > dec_frac:
+            # pos_value does NOT contribute
+            # to decimal fraction
+            bin_frac = bin_frac + '0'
+        else:
+            # pos_value contributes
+            # to decimal fraction
+            bin_frac = bin_frac + '1'
+            # update running_sum
+            running_sum = running_sum + pos_value
+
+    return bin_frac